Self-replicating, self-amplifying probes for detection of disease-related nucleic acid sequences

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Methods for the specific detection of nucleic acid sequences are of high importance in modern molecular biology. Enzymatic ligations are often used for diagnostic purposes, although they display some limitations. Depending on the enzymes used, ligation of RNA and modified nucleic acids is often inefficient compared to unmodified DNA. In addition, enzymatic ligation reactions are difficult to carry out in vivo. Although nonenzymatic probes are available, they lack signal amplification. Recently, Kool and co-workers have developed probes consisting of modified DNA, which were used to efficiently detect DNA and RNA target sequences by a self-ligation mechanism with high specificity against single mismatches. This nonenzymatic reaction shows some signal amplification. By utilizing these self-ligation probes, it has been possible to detect Escherichia coli by targeting ribosomal RNA in situ. The proposed research project aims at developing a new class of self-ligating probes for detection of less abundant RNA and even DNA in fixed and living cells. A novel probe design should prevent the common problem of product inhibition, enabling enhanced turnover. Furthermore, by rendering the self-ligation to occur exponentially, increased sensitivity should be gained, enabling detection of traces of pathogenic bacteria as also to sense and localize disease-related DNA and RNA sequences in human cells including single nucleotide polymorphisms, oncogenes and mis-splicing events.